No, replays in the database aren't all guaranteed to be intended routes. Some can be re-coverings after a physics change. Only after a while, we started caring to have at least one intended route when covering.
The replays aren't judged to be backroutes or intended. Judging replays, and writing this into the replay itself, is an important long-term idea.
But I think you can implement your fix. As long as it removes this most surprising shortcut, it improves Cornerstone.
-- Simon